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Fig. 1 | BMC Microbiology

Fig. 1

From: Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

Fig. 1

Bioinformatics pipeline used for data analysis. Twelve buffaloes were included in each group. After quality control, individual sequences were taxonomically classified with Kraken2 and functionally analyzed with HUMAnN2. Combined assembly was conducted with SPAdes and assembled contigs were annotated with Prokka. In parallel, binning of contigs was conducted with MetaBAT2 and such bins were phylogenetically analyzed with MAGpy. De novo assembly of proteins was carried out with PLASS. Protein sequences annotated with Prokka or assembled with PLASS were consolidated and clustered with Linclust to determine a set of non-redundant representative sequences, which were aligned against several protein databases using Diamond. All statistical comparisons were conducted with LEfSe. A description of all command lines used is in the bitbucket repository (https://github.com/buffGenomic/PipelineColBuff)

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BMC Microbiology

ISSN: 1471-2180

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